BME103:W930 Group5 l2

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| [[Image:IMG_1946.jpg|100px|thumb|Name: Dana McElwain<br>Role(s): Open PCR Machine Engineer]]
| [[Image:IMG_1946.jpg|100px|thumb|Name: Dana McElwain<br>Role(s): Open PCR Machine Engineer]]
| [[Image:008.jpg|100px|thumb|Name: Chris Anastos<br>Roles(s): R&D Scientist]]
| [[Image:008.jpg|100px|thumb|Name: Chris Anastos<br>Roles(s): R&D Scientist]]
| [[Image:|100px|thumb|Name: Michelle Nguyen<br>Role(s): R&D Scientist]]
| [[Image:MichelleN.jpg|100px|thumb|Name: Michelle Nguyen<br>Role(s): R&D Scientist]]

Revision as of 12:09, 28 November 2012

BME 103 Fall 2012 Home
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
Wiki Editing Help



Name: Andrea CarpenterRole(s): Experimental Protocol Planner
Name: Andrea Carpenter
Role(s): Experimental Protocol Planner
Name: Malik McLaurinRole(s): Open PCR Machine Engineer
Name: Malik McLaurin
Role(s): Open PCR Machine Engineer
Name: Dana McElwainRole(s): Open PCR Machine Engineer
Name: Dana McElwain
Role(s): Open PCR Machine Engineer
Name: Chris AnastosRoles(s): R&D Scientist
Name: Chris Anastos
Roles(s): R&D Scientist
Name: Michelle NguyenRole(s): R&D Scientist
Name: Michelle Nguyen
Role(s): R&D Scientist


Thermal Cycler Engineering

Our re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.

System Design

Key Features
The following picture is a simple change in the design of the large exterior screw located on the top of the Open PCR lid:




Supplied in Kit

Supplies Amount
Micro Test Tubes50
glass slides25
Transfer Pipettes50
PCR Master Mix6 samples (598.8μL total)
Positive Control Solution*1 sample (100.0μL***)
Negative Control Solution**1 sample (100.0μL***)
PCR Machine1

(*)Positive control consists of calf thymus DNA
(**)Negative control simply consists of a blank solution of water
(***)Already mixed with PCR master mix

Included in Fluorimeter Package:

Supplies Amount
Smart phone stand1
LCD Box1
Light box1
Sybr green solution500.0μL

Components of PCR master mix:

DNA Solution Component Amount
Patient’s Template DNA*0.2μL
10μM forward primer1.0μL
10μM reverse primer1.0μL
Promega GoTaq master mix50.0μL

(*)Not actually included in kit, but must be added to the master mix by the user.

Supplied by User

Supplies Amount
Smart Phone with Camera1
Patient's Template DNA6 samples (0.2μL each)
External Computer1
Image J Software1
Open PCR Software1
Gloves1 pair
Fine Point Sharpie1
Lab Coat1

PCR Protocol

DNA Measurement Protocol

  1. Remove the 2 controls and the 6 samples (or more if the user added more of their own samples) from the PCR tray after the PCR protocol has finished.
  2. Using a fine point sharpie, label each

Research and Development

Background on Disease Markers

For this experiment, our group chose to take an in-depth look at acute myeloid leukemia (AML). AML is a type of cancer that begins inside the bone marrow. The immune system of the human body is ultimately affected by AML, as bone marrow helps fight infections. The white blood cells that grow and form in bone marrow are turned into cancerous cells; the cells grow very quickly and sporadically, thus replacing healthy white blood cells. Our reference single nucleotide polymorphism associated with acute myeloid leukemia is rs121912500. In this SNP, the pathogenic allele for AML is classified as a single nucleotide variation. This means that only one nucleotide is altered in the allele causing AML. This variation results in a missense mutation.

The pathogenic allele origin for AML is a C-germline to A-germline mutation. In other words, cytosine is changed to adenine at chromosomal position 36259238 on chromosome 21. Also, it is important to mention that the gene associated with AML is RUNX1; a mutation in RUNX1 can even be associated with breast cancer. The DNA we are concerned with is GCAGCATGGTGGAGGTGCTGGCCGAC[A/C]ACCCGGGCGAGCTGGTGCGCACCGA.

Another form of leukemia, transient myeloproliferative leukemia, is identified with a heterozygous C to A transversion as well. In a 2002 leukemia journal written by Taketani et al., the RUNX1 gene was screened and studied in a sample group of 46 patients with down syndrome. These patients all had hematologic malignancies, meaning they were all affected by different cancers associated with bone marrow. Out of these patients, was identified with this C to A transversion and diagnosed with transient myeloproliferative leukemia 5 days after birth. However, the newborn patient died 12 months after birth. The newborn was never screened for acute myeloid leukemia. The conclusion here is that if there is an identified C-A mutation regarding the RUNX1 gene, then AML should be screened and tested for. An amniotic fluid test should be given to pregnant women in order to determine if their children carry the mutated gene associated with acute myeloid leukemia.

Primer Design

In the above sequence for the acute myeloid leukemia disease allele, the mutation occurs at the A/C mutation site. For a non-disease bearing allele, C will be coded in the sequence. For the disease bearing allele, A will be coded in place of C, resulting in a missense mutation. Forward primer sequence (while reading left to right, 5'-3', position indicated is 36259238 to 36259238): GGTCGGCCAGCACCTCCACC

Reverse primer sequence (while reading right to left, 3'-5', 200 coordinates/base pairs to the right): CGTTTGTCGAGGATGGTCTG

The diseased allele will give a PCR product because it will be amplified by using the created primers in the polymerase chain reaction. The non-disease allele will not give a PCR product because the primers are specifically coded for the disease-carrying allele containing the wrongfully inserted adenine.


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